remove requirements in setup #4
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Test Binette | |
| on: [push] #to any branch | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.8] #["3.8", "3.9", "3.10"] | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| # # Setting up miniconda | |
| # - uses: conda-incubator/setup-miniconda@v2 | |
| # with: | |
| # mamba-version: "*" | |
| # python-version: ${{ matrix.python-version }} | |
| # channels: conda-forge,bioconda,defaults | |
| # activate-environment: test | |
| # - name: Set up test environment | |
| # shell: bash -l {0} | |
| # run: | | |
| # mamba install -y binette | |
| # - name: check installation | |
| # shell: bash -l {0} | |
| # run: | | |
| # python --version | |
| # binette --version | |
| # - uses: actions/checkout@v3 | |
| # - name: Set up Python ${{ matrix.python-version }} | |
| # uses: actions/setup-python@v3 | |
| # with: | |
| # python-version: ${{ matrix.python-version }} | |
| # - name: Add conda to system path | |
| # run: | | |
| # # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| # echo $CONDA/bin >> $GITHUB_PATH | |
| # - name: Install mamba | |
| # run: | | |
| # conda install -c conda-forge mamba | |
| # - name: Install binette dependencies | |
| # run: | | |
| # mamba env update --file binette.yaml --name base | |
| # Setting up miniconda | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda,defaults | |
| environment-file: binette.yaml | |
| activate-environment: binette | |
| - name: Install binette | |
| run: | | |
| pip install . | |
| binette -h | |
| - name: Lint with flake8 | |
| run: | | |
| conda install flake8 | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| mamba install pytest | |
| pytestconda | |
| - name: Download test data | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: genotoul-bioinfo/Binette_TestData | |
| path: test_data | |
| - name: Run simple test case | |
| run: | | |
| cd test_data | |
| binette -b binning_results/* --contigs all_contigs.fna --checkm2_db checkm2_tiny_db/checkm2_tiny_db.dmnd -v -o test_results | |
| - name: Compare results with expectation | |
| run: | | |
| cd test_data | |
| head expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv | |
| python scripts/compare_results.py expected_results/final_bins_quality_reports.tsv test_results/final_bins_quality_reports.tsv |